FileNotFoundError in maisi_train_vae_tutorial.ipynb

[KumoLiu]

[2025-04-01T20:31:44.899Z] Running ./generation/maisi/maisi_train_vae_tutorial.ipynb

[2025-04-01T20:31:44.899Z] Checking PEP8 compliance...

[2025-04-01T20:31:45.460Z] Running notebook...

[2025-04-01T20:31:55.399Z] MONAI version: 1.4.1rc1+38.g4986d7ff

[2025-04-01T20:31:55.399Z] Numpy version: 1.26.4

[2025-04-01T20:31:55.399Z] Pytorch version: 2.6.0+cu124

[2025-04-01T20:31:55.399Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False

[2025-04-01T20:31:55.399Z] MONAI rev id: 4986d7ffd2d351c9d66de0e0329884b1a26d5500

[2025-04-01T20:31:55.399Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py

[2025-04-01T20:31:55.399Z] 

[2025-04-01T20:31:55.399Z] Optional dependencies:

[2025-04-01T20:31:55.399Z] Pytorch Ignite version: 0.4.11

[2025-04-01T20:31:55.399Z] ITK version: 5.4.3

[2025-04-01T20:31:55.399Z] Nibabel version: 5.3.2

[2025-04-01T20:31:55.399Z] scikit-image version: 0.19.3

[2025-04-01T20:31:55.399Z] scipy version: 1.14.0

[2025-04-01T20:31:55.399Z] Pillow version: 11.2.0

[2025-04-01T20:31:55.399Z] Tensorboard version: 2.16.2

[2025-04-01T20:31:55.399Z] gdown version: 5.2.0

[2025-04-01T20:31:55.399Z] TorchVision version: 0.21.0+cu124

[2025-04-01T20:31:55.399Z] tqdm version: 4.66.5

[2025-04-01T20:31:55.399Z] lmdb version: 1.6.2

[2025-04-01T20:31:55.399Z] psutil version: 6.0.0

[2025-04-01T20:31:55.399Z] pandas version: 2.2.2

[2025-04-01T20:31:55.399Z] einops version: 0.8.0

[2025-04-01T20:31:55.399Z] transformers version: 4.40.2

[2025-04-01T20:31:55.399Z] mlflow version: 2.21.2

[2025-04-01T20:31:55.399Z] pynrrd version: 1.1.3

[2025-04-01T20:31:55.399Z] clearml version: 1.18.0

[2025-04-01T20:31:55.399Z] 

[2025-04-01T20:31:55.399Z] For details about installing the optional dependencies, please visit:

[2025-04-01T20:31:55.399Z]     https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

[2025-04-01T20:31:55.399Z] 

[2025-04-01T20:31:57.286Z] papermill  --progress-bar --log-output -k python3

[2025-04-01T20:31:57.845Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : -

[2025-04-01T20:31:57.845Z]   warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}")

[2025-04-01T20:36:43.746Z] 
Executing:   0%|          | 0/29 [00:00<?, ?cell/s]
Executing:   3%|▎         | 1/29 [00:00<00:26,  1.04cell/s]
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Executing:  17%|█▋        | 5/29 [00:20<01:44,  4.37s/cell]
Executing:  31%|███       | 9/29 [04:42<13:32, 40.61s/cell]
Executing:  45%|████▍     | 13/29 [04:42<05:51, 22.00s/cell]
Executing:  45%|████▍     | 13/29 [04:45<05:51, 21.95s/cell]

[2025-04-01T20:36:43.746Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : -

[2025-04-01T20:36:43.746Z]   warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}")

[2025-04-01T20:36:43.746Z] Traceback (most recent call last):

[2025-04-01T20:36:43.746Z]   File "/usr/local/bin/papermill", line 8, in <module>

[2025-04-01T20:36:43.746Z]     sys.exit(papermill())

[2025-04-01T20:36:43.746Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__

[2025-04-01T20:36:43.746Z]     return self.main(*args, **kwargs)

[2025-04-01T20:36:43.746Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main

[2025-04-01T20:36:43.746Z]     rv = self.invoke(ctx)

[2025-04-01T20:36:43.746Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke

[2025-04-01T20:36:43.746Z]     return ctx.invoke(self.callback, **ctx.params)

[2025-04-01T20:36:43.746Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke

[2025-04-01T20:36:43.746Z]     return __callback(*args, **kwargs)

[2025-04-01T20:36:43.746Z]   File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func

[2025-04-01T20:36:43.746Z]     return f(get_current_context(), *args, **kwargs)

[2025-04-01T20:36:43.746Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 235, in papermill

[2025-04-01T20:36:43.746Z]     execute_notebook(

[2025-04-01T20:36:43.746Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 131, in execute_notebook

[2025-04-01T20:36:43.746Z]     raise_for_execution_errors(nb, output_path)

[2025-04-01T20:36:43.746Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 251, in raise_for_execution_errors

[2025-04-01T20:36:43.746Z]     raise error

[2025-04-01T20:36:43.746Z] papermill.exceptions.PapermillExecutionError: 

[2025-04-01T20:36:43.746Z] ---------------------------------------------------------------------------

[2025-04-01T20:36:43.746Z] Exception encountered at "In [6]":

[2025-04-01T20:36:43.746Z] ---------------------------------------------------------------------------

[2025-04-01T20:36:43.746Z] FileNotFoundError                         Traceback (most recent call last)

[2025-04-01T20:36:43.746Z] Cell In[6], line 2

[2025-04-01T20:36:43.746Z]       1 config_file = "./configs/config_maisi.json"

[2025-04-01T20:36:43.746Z] ----> 2 config_dict = json.load(open(config_file, "r"))

[2025-04-01T20:36:43.746Z]       3 for k, v in config_dict.items():

[2025-04-01T20:36:43.746Z]       4     setattr(args, k, v)

[2025-04-01T20:36:43.746Z] 

[2025-04-01T20:36:43.746Z] File /usr/local/lib/python3.10/dist-packages/IPython/core/interactiveshell.py:324, in _modified_open(file, *args, **kwargs)

[2025-04-01T20:36:43.746Z]     317 if file in {0, 1, 2}:

[2025-04-01T20:36:43.746Z]     318     raise ValueError(

[2025-04-01T20:36:43.746Z]     319         f"IPython won't let you open fd={file} by default "

[2025-04-01T20:36:43.746Z]     320         "as it is likely to crash IPython. If you know what you are doing, "

[2025-04-01T20:36:43.746Z]     321         "you can use builtins' open."

[2025-04-01T20:36:43.746Z]     322     )

[2025-04-01T20:36:43.746Z] --> 324 return io_open(file, *args, **kwargs)

[2025-04-01T20:36:43.746Z] 

[2025-04-01T20:36:43.746Z] FileNotFoundError: [Errno 2] No such file or directory: './configs/config_maisi.json'

[KumoLiu]

[2025-04-01T20:31:01.618Z] Running ./generation/maisi/data/mask_augmentation_example.ipynb

[2025-04-01T20:31:01.618Z] Checking PEP8 compliance...

[2025-04-01T20:31:02.179Z] Running notebook...

[2025-04-01T20:31:12.114Z] MONAI version: 1.4.1rc1+38.g4986d7ff

[2025-04-01T20:31:12.114Z] Numpy version: 1.26.4

[2025-04-01T20:31:12.114Z] Pytorch version: 2.6.0+cu124

[2025-04-01T20:31:12.114Z] MONAI flags: HAS_EXT = False, USE_COMPILED = False, USE_META_DICT = False

[2025-04-01T20:31:12.114Z] MONAI rev id: 4986d7ffd2d351c9d66de0e0329884b1a26d5500

[2025-04-01T20:31:12.114Z] MONAI __file__: /home/jenkins/agent/workspace/Monai-notebooks/MONAI/monai/__init__.py

[2025-04-01T20:31:12.114Z] 

[2025-04-01T20:31:12.114Z] Optional dependencies:

[2025-04-01T20:31:12.114Z] Pytorch Ignite version: 0.4.11

[2025-04-01T20:31:12.114Z] ITK version: 5.4.3

[2025-04-01T20:31:12.114Z] Nibabel version: 5.3.2

[2025-04-01T20:31:12.114Z] scikit-image version: 0.19.3

[2025-04-01T20:31:12.114Z] scipy version: 1.14.0

[2025-04-01T20:31:12.114Z] Pillow version: 11.2.0

[2025-04-01T20:31:12.114Z] Tensorboard version: 2.16.2

[2025-04-01T20:31:12.114Z] gdown version: 5.2.0

[2025-04-01T20:31:12.114Z] TorchVision version: 0.21.0+cu124

[2025-04-01T20:31:12.114Z] tqdm version: 4.66.5

[2025-04-01T20:31:12.114Z] lmdb version: 1.6.2

[2025-04-01T20:31:12.114Z] psutil version: 6.0.0

[2025-04-01T20:31:12.114Z] pandas version: 2.2.2

[2025-04-01T20:31:12.114Z] einops version: 0.8.0

[2025-04-01T20:31:12.114Z] transformers version: 4.40.2

[2025-04-01T20:31:12.114Z] mlflow version: 2.21.2

[2025-04-01T20:31:12.114Z] pynrrd version: 1.1.3

[2025-04-01T20:31:12.114Z] clearml version: 1.18.0

[2025-04-01T20:31:12.114Z] 

[2025-04-01T20:31:12.114Z] For details about installing the optional dependencies, please visit:

[2025-04-01T20:31:12.114Z]     https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies

[2025-04-01T20:31:12.114Z] 

[2025-04-01T20:31:13.477Z] papermill  --progress-bar --log-output -k python3

[2025-04-01T20:31:14.399Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : -

[2025-04-01T20:31:14.399Z]   warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}")

[2025-04-01T20:31:44.898Z] 
Executing:   0%|          | 0/13 [00:00<?, ?cell/s]
Executing:   8%|▊         | 1/13 [00:00<00:11,  1.08cell/s]
Executing:  23%|██▎       | 3/13 [00:12<00:44,  4.42s/cell]
Executing:  38%|███▊      | 5/13 [00:20<00:33,  4.24s/cell]
Executing:  54%|█████▍    | 7/13 [00:26<00:21,  3.65s/cell]
Executing:  69%|██████▉   | 9/13 [00:27<00:09,  2.46s/cell]
Executing:  85%|████████▍ | 11/13 [00:27<00:03,  1.65s/cell]
Executing:  85%|████████▍ | 11/13 [00:30<00:05,  2.75s/cell]

[2025-04-01T20:31:44.898Z] /usr/local/lib/python3.10/dist-packages/papermill/iorw.py:149: UserWarning: the file is not specified with any extension : -

[2025-04-01T20:31:44.898Z]   warnings.warn(f"the file is not specified with any extension : {os.path.basename(path)}")

[2025-04-01T20:31:44.898Z] Traceback (most recent call last):

[2025-04-01T20:31:44.898Z]   File "/usr/local/bin/papermill", line 8, in <module>

[2025-04-01T20:31:44.898Z]     sys.exit(papermill())

[2025-04-01T20:31:44.899Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1157, in __call__

[2025-04-01T20:31:44.899Z]     return self.main(*args, **kwargs)

[2025-04-01T20:31:44.899Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1078, in main

[2025-04-01T20:31:44.899Z]     rv = self.invoke(ctx)

[2025-04-01T20:31:44.899Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 1434, in invoke

[2025-04-01T20:31:44.899Z]     return ctx.invoke(self.callback, **ctx.params)

[2025-04-01T20:31:44.899Z]   File "/usr/local/lib/python3.10/dist-packages/click/core.py", line 783, in invoke

[2025-04-01T20:31:44.899Z]     return __callback(*args, **kwargs)

[2025-04-01T20:31:44.899Z]   File "/usr/local/lib/python3.10/dist-packages/click/decorators.py", line 33, in new_func

[2025-04-01T20:31:44.899Z]     return f(get_current_context(), *args, **kwargs)

[2025-04-01T20:31:44.899Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/cli.py", line 235, in papermill

[2025-04-01T20:31:44.899Z]     execute_notebook(

[2025-04-01T20:31:44.899Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 131, in execute_notebook

[2025-04-01T20:31:44.899Z]     raise_for_execution_errors(nb, output_path)

[2025-04-01T20:31:44.899Z]   File "/usr/local/lib/python3.10/dist-packages/papermill/execute.py", line 251, in raise_for_execution_errors

[2025-04-01T20:31:44.899Z]     raise error

[2025-04-01T20:31:44.899Z] papermill.exceptions.PapermillExecutionError: 

[2025-04-01T20:31:44.899Z] ---------------------------------------------------------------------------

[2025-04-01T20:31:44.899Z] Exception encountered at "In [5]":

[2025-04-01T20:31:44.899Z] ---------------------------------------------------------------------------

[2025-04-01T20:31:44.899Z] TypeError                                 Traceback (most recent call last)

[2025-04-01T20:31:44.899Z] Cell In[5], line 1

[2025-04-01T20:31:44.899Z] ----> 1 volume_aug = augmentation(volume.unsqueeze(0), volume_shape).squeeze(0)

[2025-04-01T20:31:44.899Z] 

[2025-04-01T20:31:44.899Z] TypeError: augmentation() missing 1 required positional argument: 'random_seed'

[KumoLiu]

Hi @Can-Zhao, could you please also update these two tutorials related to the change introduced by this PR: #1953
Thanks!

[Can-Zhao]

Please see https://github.com/Project-MONAI/tutorials/pull/1967/files